After becoming commerce secretary, Wilbur L. Ross Jr. retained investments in a shipping firm he once controlled that has significant business ties to a Russian oligarch subject to American sanctions and President Vladimir V. Putin’s son-in-law, according to newly disclosed documents.

The shipper, Navigator Holdings, earns millions of dollars a year transporting gas for one of its top clients, a giant Russian energy company called Sibur, whose owners include the oligarch and Mr. Putin’s family member. Despite selling off numerous other holdings to join the Trump administration and spearhead its “America first” trade policy, Mr. Ross kept an investment in Navigator, which increased its business dealings with Sibur even as the West sought to punish Russia’s energy sector over Mr. Putin’s incursions into Ukraine.

Partnerships used by Mr. Ross, whose private equity firm has long been the biggest shareholder in Navigator, have a 31 percent stake in the company. Though his personal share of that stake was reduced as he took office in February, he retained an investment in the partnerships valued between $2 million and $10 million, and stood to earn a higher share of profits as a general partner, according to his government ethics disclosure and securities filings.

Mr. Ross’s stake in Navigator has been held by a chain of companies in the Cayman Islands, one of several tax havens where much of his wealth, estimated at more than $2 billion, has been tied to similar investment vehicles. Details of these arrangements surfaced in a cache of leaked files from Appleby, one of the world’s largest offshore law firms, which administered some 50 companies and partnerships in the Caymans and elsewhere connected to Mr. Ross.

The Appleby documents, obtained by the German newspaper Süddeutsche Zeitung, were shared with the International Consortium of Investigative Journalists and other media organizations, including The New York Times. They show how the Bermuda-based Appleby worked to help the wealthy elite, from Russian oligarchs to Middle Eastern princes, as well as multinational corporations like Apple and Nike, avoid billions of dollars in taxes.

In addition to Mr. Ross, the files contain references to other members of the Trump administration, including Gary D. Cohn, the chief economic adviser who was associated with 22 Bermuda entities while an executive at Goldman Sachs, and Secretary of State Rex W. Tillerson, who was a director of a Bermuda-based joint venture with the government of Yemen when he ran Exxon Mobil’s operations there. There is no evidence of illegality in any of their dealings.

Mr. Ross emerges as a particularly valued client for the offshore law firm, whose records provide more insight into his financial holdings beyond the public ethics disclosures he made upon joining the Trump administration. His ethics agreement filed in January listed the partnerships he intended to keep, but not the investments they held. Previously, Navigator had been mentioned in a separate, 57-page description of his holdings for the year that ended in December 2016, but with no hint of its ties to Sibur.

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Mr. Ross during his confirmation hearing in January.Credit
Al Drago/The New York Times

Sibur’s top ownership — including Gennady Timchenko, who is Mr. Putin’s friend and judo partner and is subject to American sanctions, and Kirill Shamalov, who is married to the Russian president’s youngest daughter — makes it “a company with crony connections” in Moscow, said Daniel Fried, a Russia expert who served in senior State Department posts in Republican and Democratic administrations.

Another of Navigator’s major customers is PDVSA, the Venezuelan state oil company, controlled by the authoritarian regime of Nicolás Maduro. The Trump administration imposed sanctions on PDVSA this summer.

In a written response to questions by the Times, James Rockas, a spokesman for Mr. Ross, said that Navigator’s relationship with Sibur began before Mr. Ross joined the board in March 2012, and that he had never met the Russian oligarchs who are Sibur’s major shareholders. Public records show that Mr. Ross’s firm became a major investor in Navigator in November 2011, three months before the company chartered its first ships to Sibur.

“Sibur was not under sanctions at the time the contract was signed and is still not subject to sanctions,” Mr. Rockas said.

More broadly, he said that Mr. Ross “recuses himself from any matters focused on transoceanic shipping vessels, but has been generally supportive of the administration’s sanctions of Russian and Venezuelan entities.”

“Secretary Ross has never had to seek, nor received, any ethics exemption,” Mr. Rockas said, “and he works closely with Commerce Department ethics officials to ensure the highest ethical standards.”

It is perhaps unsurprising that Navigator would have a relationship with a major Russian company during Mr. Ross’s tenure. Much like President Trump, whose company sought approval for a hotel project in Moscow as recently as last year, Mr. Ross has long shown an appreciation for the untapped potential of Russian markets when seeking investment opportunities. His involvement there dates at least to the 1990s, when he was appointed by President Bill Clinton to the board of the U.S. Russia Investment Fund, established to promote American business interests in Russia.

In addition to Navigator, his firm also acquired a German rail car company, VTG, which pursued an expansion strategy in Russia before Mr. Ross sold his stake in 2016. And Mr. Ross led a private bailout of the Bank of Cyprus, long regarded as a favorite financial haven of wealthy Russians, after the worldwide economic crisis crippled the Cypriot banking system.

In the wake of reports of Russian interference in the United States presidential election, multiple investigations have explored potential business ties between Russia and members of the Trump administration. While several Trump campaign and business associates have come under scrutiny, until now no business connections have been reported between senior administration officials and members of Mr. Putin’s family or inner circle.

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Mr. Ross led a private bailout of the Bank of Cyprus, considered a favorite financial haven of wealthy Russians, after the economic crisis crippled the Cypriot banking system.Credit
Sean Gallup/Getty Images

During Mr. Ross’s confirmation process, he was asked repeatedly about his business ties to Russia, mostly related to his former role as vice chairman of the Bank of Cyprus, where he dealt with Russian investors but also forced some of them out of the bank. He was also asked about his investment in another shipping company, Diamond S, and whether its dealings with China could pose a conflict with his government duties. But he faced no questions about Navigator and its significant financial relationship with Sibur.

Mr. Rockas did not respond to questions about the current status of Mr. Ross’s investment. If Mr. Ross stands to benefit, albeit indirectly, from a Russian firm controlled by members of Mr. Putin’s inner circle, it poses a potential conflict with his role as the lead cabinet member on trade policy, ethics experts said. Richard W. Painter, who served as chief ethics lawyer in the George W. Bush White House and has emerged as a frequent critic of the Trump administration, said that while Mr. Ross’s continued investment in Navigator would not violate any laws, it created other ethical concerns.

“Apart from those legal issues,” Mr. Painter said, “I’d be very concerned that someone in the U.S. government was making money from dealing with the Russians.”

As for Navigator, its leadership sees blue skies ahead with one of its key investors now at the helm of American trade policy.

On Nov. 30 of last year, hours after being nominated as commerce secretary, Mr. Ross celebrated at Gramercy Tavern, an upscale Manhattan restaurant, at an event hosted by Navigator. He and David J. Butters, Navigator’s chief executive, arrived early to a private room and had a chat.

“Your interest is aligned to mine,” Mr. Butters recalls Mr. Ross saying, according to Bloomberg Businessweek. “The U.S. economy will grow, and Navigator will be a beneficiary.”

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Looking East

Mr. Ross’s foray into transoceanic shipping took off in 2011, when his private equity firm, WL Ross & Co., assembled teams of investors to acquire major stakes in Diamond S Shipping and Navigator Holdings. Both firms specialized in chartering tankers to petroleum companies that need to move gas, oil and petrochemicals around the world. With Mr. Ross’s involvement, they would expand their business interests in China and Russia.

The investments — eventually totaling more than $600 million in Diamond S and about $240 million in Navigator — were in keeping with Mr. Ross’s strategy of scooping up shares in undervalued companies and turning them around. It is a business model that has earned Mr. Ross, a 79-year-old Ivy League-educated son of middle-class parents from New Jersey, the sobriquet of “king of bankruptcy.”

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Over a lengthy investment career that included a stint running the bankruptcy advisory practice at the British banking firm Rothschild, he has breathed new life into textile, steel and auto-part businesses. While at Rothschild in the early 1990s, he led a group of bondholders in a restructuring of the floundering Trump casinos in Atlantic City, preserving a stake for Mr. Trump because, as he reportedly assured disgruntled investors, the Trump name was “still very much an asset.”

Mr. Ross’s business practices have occasionally drawn criticism for moving American jobs overseas in an effort to improve profits. A Reuters analysis of Labor Department statistics found that his takeovers shifted 2,700 jobs in automotive, textiles and mortgage finance to, among other places, China, India, Mexico and Nicaragua.

In the statement to The Times, Mr. Ross’s spokesman said, “Private equity firms have a responsibility to their investors to optimize corporate structures, and Secretary Ross has decades of experience that he is now using to benefit American workers.”

As worldwide shipping concerns, Diamond S and Navigator did not have much of a labor footprint in the United States when Mr. Ross and his investors took over. But the way both companies did business would pose potential conflicts with American interests in other ways.

Alongside Mr. Ross, another large investor in Diamond S was a company controlled by the Chinese government, according to securities filings. And Navigator signed a charter agreement with Sibur shortly after Mr. Ross’s firm made its investment. Sibur said in a statement that any negotiations with Navigator over the years were carried out by its executives, not its major shareholders, and that “no meetings were held with Mr. Ross.”

Initially, Navigator chartered two vessels to Sibur, and later increased the fleet to four. The relationship proved to be so profitable that Navigator’s chief executive, Mr. Butters, told investors in a 2016 conference call how Navigator benefited as Sibur beat out American competitors in the growing European energy market.

“Russia is pipelining as much natural gas as needed into Europe, and liquids are being shipped into all areas of the continent in increasing amounts, all in competition with longer-haul U.S. exports,” Mr. Butters said.

Putin Connections

As one of the largest gas companies in Russia, Sibur is not just any private business.

It was created by the Russian government and maintains a close dependency on Moscow, even after its sale in 2010 to Mr. Timchenko and Leonid Mikhelson. The two men are typical of Russian moguls who have benefited from state-owned assets and are expected to remain loyal to the Putin government, said Amos J. Hochstein, a top energy diplomat under the Obama administration.

“When you start doing business with Russian energy companies like Gazprom and Sibur, you’re not just getting into bed with the company,” Mr. Hochstein said. “You’re getting into bed with the Russian state.”

The ties to the Russian president, however, proved to be a double-edged sword for Sibur’s owners. In 2014, after Russia seized Crimea from Ukraine, American and Western allies imposed economic sanctions on key Putin associates, including Mr. Timchenko. A few months later, the United States barred banks from providing new financing to another gas company, Novatek, belonging to Mr. Mikhelson.

Sibur itself was not targeted. But financial institutions, including Bank of America and the Royal Bank of Scotland, backed away from loans to the company, according to news reports at the time. Moscow stepped in to help in May 2014, when a government-backed financial consortium bought a shipping terminal from Sibur and pledged to expand export capacity, while allowing Sibur to remain the terminal’s sole exporter of gas.

Then, in September 2014, as sanctions pressure was growing, Mr. Timchenko reduced his holdings in Sibur by selling a 17 percent stake to a junior shareholder, Mr. Shamalov. A year earlier, Mr. Shamalov, whose father is a friend and former business partner of Mr. Putin’s, had married the Russian president’s daughter Katerina. His Sibur purchase, which pushed the 32-year-old Mr. Shamalov’s investment to more than 20 percent of the company, was financed by a $1.3 billion loan from the state-backed Gazprombank. Mr. Shamalov sold part of his stake in April, reducing it to 3.9 percent.

Most of these financial machinations were carried out through offshore companies on Cyprus, where Mr. Mikhelson and Mr. Timchenko held their investments in Sibur and did business with several Cypriot banks. During the summer of 2014, Mr. Ross had become the Bank of Cyprus’s vice chairman, though there is no indication that he crossed paths with the two oligarchs during his tenure there.

His position at the bank required him to step down from the board of Navigator, however, even as he retained his investment in the company. His close associate at WL Ross & Co., Wendy L. Teramoto, took his place at Navigator and, later, left to join Mr. Ross as chief of staff at the Commerce Department.

Despite the reluctance of Western financial institutions to do business with Sibur and its owners, Navigator’s relationship with Sibur continued to grow.

From 2014 to 2015, the portion of Navigator’s total revenue that came from Sibur jumped to 9.1 percent from 5.3 percent, making the company one of its top five clients, according to securities filings, before dipping to 7.9 percent last year.

Ethics Disclosures

As WL Ross & Co. expanded over the years, it used Appleby, the offshore specialist, to set up an increasing number of entities in tax havens, many in the Cayman Islands. This British territory in the Caribbean levies no corporate or personal income tax on money earned outside its jurisdiction, and requires little disclosure of corporate ownership. By 2014, Mr. Ross and his investment company were among Appleby’s top 20 clients.

After he was nominated as commerce secretary, Mr. Ross filed an agreement with the federal Office of Government Ethics saying he would resign from WL Ross & Co. and divest from 80 companies and partnerships, but would keep a stake in nine others that held assets in “real estate financing and mortgage lending” and “transoceanic shipping.” The underlying assets were not specified.

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Mr. Ross at Trump Tower in Manhattan last year. Leaked files from an offshore law firm have provided insight into his financial holdings beyond the ethics disclosures he made on joining the Trump administration.Credit
Sam Hodgson for The New York Times

His financial disclosure form offered more detail, including a list of assets that had been held by each of the partnerships that he retained. Navigator Holdings appeared in connection with four Appleby-managed Cayman partnerships. Mr. Ross’s ethics filing valued his stake in those partnerships at between $2.05 million and $10.1 million, a fraction of the partnerships’ combined 31.5 percent stake in Navigator, which, based on the firm’s recent stock price, was worth roughly $179 million. In all, WL Ross & Co. remains Navigator’s largest shareholder, according to the shipping company’s most recent annual report.

Federal ethics law requires officials to recuse themselves from matters that would have “a direct and predictable” effect on their financial interests or cause a reasonable doubt about their impartiality. During his confirmation hearings, Mr. Ross sought to reassure senators that he would avoid any conflicts of interest between his continued business holdings and his cabinet post.

“I intend to be quite scrupulous about recusal and any topic where there is the slightest scintilla of doubt,” he said.

Sasha Chavkin and Martha M. Hamilton are reporters for the International Consortium of Investigative Journalists.

A version of this article appears in print on November 6, 2017, on Page A1 of the New York edition with the headline: A Complex Paper Trail: Blurring Kremlin’s Ties To Key U.S. Businesses. Order Reprints|Today's Paper|Subscribe